jTEI articles can have footnotes. Since no other notes are supported, the encoding is fairly simple: just add a note element at the place where you want to insert the footnote in the text. No further attributes are required: numbering is catered for at rendering time. Notes can contain plain text or paragraphs. No block-level elements are allowed:
<p>There are essentially two pointing mechanisms TEI employs to implement its graph data structure: XPath, used in the <att>match</att> attribute, <note> <p>See <ptr target="http://www.tei-c.org/Vault/P5/2.2.0/doc/tei-p5-doc/en/html/ref-att.scoping.html"/> </p> </note> and URIs, which can indicate documents, or (using fragment identifiers) elements in the current document which have <att>xml:id</att> attributes.</p>